I have a clarification of which file to use from Xenbas (laevis). From this link-http://www.xenbase.org/other/static/ftpDatafiles.jsp I think I will use primary gene models (FASTA) file for alignment and gene models (gff3) as GFF3 for annotation. Am I correct? I am doing RNAseq alignment with HISAT.
Here is screen shot of latest genome:
X. laevis v9.1 genome assembly[readme]FASTA Gene Model(s): 22.214.171.124 [readme] primary gene models (gff3) primary gene models (FASTA) gene models (gff3) peptide(FASTA) For the latest versions browse theXenbase FTP site